Convert change in probability to probability / odds

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: effectsize
 Title: Indices of Effect Size
-Version: 1.0.1.1
+Version: 1.0.1.2
 Authors@R:
     c(person(given = "Mattan S.",
              family = "Ben-Shachar",

NAMESPACE

@@ -35,8 +35,10 @@ S3method(interpret,effectsize_table)
 S3method(interpret,lavaan)
 S3method(interpret,numeric)
 S3method(interpret,performance_lavaan)
-S3method(odds_to_probs,data.frame)
-S3method(odds_to_probs,numeric)
+S3method(oddsratio_to_arr,default)
+S3method(oddsratio_to_arr,numeric)
+S3method(oddsratio_to_nnt,default)
+S3method(oddsratio_to_nnt,numeric)
 S3method(oddsratio_to_riskratio,default)
 S3method(oddsratio_to_riskratio,numeric)
 S3method(plot,effectsize_table)
@@ -48,13 +50,17 @@ S3method(print_html,effectsize_table)
 S3method(print_html,rules)
 S3method(print_md,effectsize_table)
 S3method(print_md,rules)
-S3method(probs_to_odds,data.frame)
-S3method(probs_to_odds,numeric)
 S3method(r2_semipartial,lm)
 S3method(rb_to_p_superiority,effectsize_difference)
 S3method(rb_to_p_superiority,numeric)
 S3method(rb_to_wmw_odds,effectsize_difference)
 S3method(rb_to_wmw_odds,numeric)
+S3method(riskratio_to_arr,default)
+S3method(riskratio_to_arr,numeric)
+S3method(riskratio_to_nnt,default)
+S3method(riskratio_to_nnt,numeric)
+S3method(riskratio_to_oddsratio,default)
+S3method(riskratio_to_oddsratio,numeric)
 export(.es_aov_simple)
 export(.es_aov_strata)
 export(.es_aov_table)
@@ -70,6 +76,7 @@ export(arr)
 export(arr_to_logoddsratio)
 export(arr_to_nnt)
 export(arr_to_oddsratio)
+export(arr_to_probs)
 export(arr_to_riskratio)
 export(c_to_w)
 export(chisq_to_cohens_w)
@@ -88,14 +95,6 @@ export(cohens_u1)
 export(cohens_u2)
 export(cohens_u3)
 export(cohens_w)
-export(convert_d_to_oddsratio)
-export(convert_d_to_r)
-export(convert_odds_to_probs)
-export(convert_oddsratio_to_d)
-export(convert_oddsratio_to_r)
-export(convert_probs_to_odds)
-export(convert_r_to_d)
-export(convert_r_to_oddsratio)
 export(cov_pooled)
 export(cramers_v)
 export(d_to_logoddsratio)
@@ -165,6 +164,7 @@ export(kendalls_w)
 export(logoddsratio_to_arr)
 export(logoddsratio_to_d)
 export(logoddsratio_to_nnt)
+export(logoddsratio_to_probs)
 export(logoddsratio_to_r)
 export(logoddsratio_to_riskratio)
 export(mad_pooled)
@@ -174,12 +174,14 @@ export(nnt)
 export(nnt_to_arr)
 export(nnt_to_logoddsratio)
 export(nnt_to_oddsratio)
+export(nnt_to_probs)
 export(nnt_to_riskratio)
 export(odds_to_probs)
 export(oddsratio)
 export(oddsratio_to_arr)
 export(oddsratio_to_d)
 export(oddsratio_to_nnt)
+export(oddsratio_to_probs)
 export(oddsratio_to_r)
 export(oddsratio_to_riskratio)
 export(omega_squared)
@@ -207,6 +209,7 @@ export(riskratio_to_arr)
 export(riskratio_to_logoddsratio)
 export(riskratio_to_nnt)
 export(riskratio_to_oddsratio)
+export(riskratio_to_probs)
 export(rm_d)
 export(rules)
 export(sd_pooled)

NEWS.md

@@ -2,8 +2,20 @@
 
 ## New features
 
+- `oddsratio_to_*()` and `riskratio_to_*()` can now convert binomial models with logit- or log-links (respectively) to any of RR, OR, ARR, NNT.
+- New functions to convert between measures of change in probabilities and probabilities. See `?oddsratio_to_probs` for all available functions.
 - `effetsize()` and friends support `datawizard::data_tabulate()` objects as inputs.
 
+## Changes
+
+`riskratio_to_*()` now returns `NA` if the expected risk is larger than 1. This results when impossible combinations of risk ratio `RR` and baseline risk `p0` are provided.
+
+## Breaking Changes
+
+- `probs_to_odds(<data.frame>)` and `odds_to_probs(<data.frame>)` methods has been deprecated.
+- `riskratio(log=)` argument has been deprecated.
+- `convert_*()` aliases, deprecated since March 2023, have been removed. 
+
 # effectsize 1.0.1
 
 ## New features

R/convert_between_odds_to_probs.R

@@ -3,10 +3,6 @@
 #' @param odds The *Odds* (or `log(odds)` when `log = TRUE`) to convert.
 #' @param probs Probability values to convert.
 #' @param log Take in or output log odds (such as in logistic models).
-#' @param select When a data frame is passed, character or list of of column
-#'   names to be transformed.
-#' @param exclude When a data frame is passed, character or list of column names
-#'   to be excluded from transformation.
 #' @param ... Arguments passed to or from other methods.
 #'
 #' @return Converted index.
@@ -22,126 +18,27 @@
 #' probs_to_odds(0.95, log = TRUE)
 #' @export
 odds_to_probs <- function(odds, log = FALSE, ...) {
-  UseMethod("odds_to_probs")
-}
+  if (is.data.frame(odds)) {
+    .deprecated_df_methods("odds_to_probs")
+  }
 
-#' @export
-odds_to_probs.numeric <- function(odds, log = FALSE, ...) {
   if (log) {
     stats::plogis(odds)
   } else {
     stats::plogis(log(odds))
   }
 }
 
-
-#' @rdname odds_to_probs
-#' @export
-odds_to_probs.data.frame <- function(odds, log = FALSE, select = NULL, exclude = NULL, ...) {
-  .odds_to_probs_df(odds = odds, log = log, select = select, exclude = exclude, ...)
-}
-
-
 #' @rdname odds_to_probs
 #' @export
 probs_to_odds <- function(probs, log = FALSE, ...) {
-  UseMethod("probs_to_odds")
-}
+  if (is.data.frame(probs)) {
+    .deprecated_df_methods("probs_to_odds")
+  }
 
-#' @export
-probs_to_odds.numeric <- function(probs, log = FALSE, ...) {
   if (log) {
     stats::qlogis(probs)
   } else {
     exp(stats::qlogis(probs))
   }
 }
-
-#' @rdname odds_to_probs
-#' @export
-probs_to_odds.data.frame <- function(probs, log = FALSE, select = NULL, exclude = NULL, ...) {
-  .odds_to_probs_df(probs = probs, log = log, select = select, exclude = exclude, ...)
-}
-
-
-
-
-
-
-
-
-
-# Data frame --------------------------------------------------------------
-
-
-
-#' @keywords internal
-.odds_to_probs_df <- function(odds = NULL, probs = NULL, log = FALSE, select = NULL, exclude = NULL, ...) {
-  # If vector
-  if (is.null(odds)) {
-    mydata <- probs
-  } else {
-    mydata <- odds
-  }
-
-  # check for formula notation, convert to character vector
-  if (inherits(select, "formula")) {
-    select <- all.vars(select)
-  }
-  if (inherits(exclude, "formula")) {
-    exclude <- all.vars(exclude)
-  }
-
-  # Variable order
-  var_order <- names(mydata)
-
-  # Keep subset
-  if (!is.null(select) && select %in% names(mydata)) {
-    select <- as.vector(select)
-    to_keep <- as.data.frame(mydata[!names(mydata) %in% select])
-    mydata <- mydata[names(mydata) %in% select]
-  } else {
-    to_keep <- NULL
-  }
-
-  # Remove exceptions
-  if (!is.null(exclude) && exclude %in% names(mydata)) {
-    exclude <- as.vector(exclude)
-    if (is.null(to_keep)) {
-      to_keep <- as.data.frame(mydata[exclude])
-    } else {
-      to_keep <- cbind(to_keep, as.data.frame(mydata[exclude]))
-    }
-
-    mydata <- mydata[!names(mydata) %in% exclude]
-  }
-
-  # Remove non-numerics
-  is_num <- vapply(mydata, is.numeric, logical(1))
-  dfother <- mydata[!is_num]
-  dfnum <- mydata[is_num]
-
-  # Tranform
-  if (is.null(odds)) {
-    dfnum <- data.frame(lapply(dfnum, probs_to_odds.numeric, log = log))
-  } else {
-    dfnum <- data.frame(lapply(dfnum, odds_to_probs.numeric, log = log))
-  }
-
-  # Add non-numerics
-  if (is.null(ncol(dfother))) {
-    mydata <- dfnum
-  } else {
-    mydata <- cbind(dfother, dfnum)
-  }
-
-  # Add exceptions
-  if (!is.null(select) || !is.null(exclude) && exists("to_keep")) {
-    mydata <- cbind(mydata, to_keep)
-  }
-
-  # Reorder
-  mydata <- mydata[var_order]
-
-  mydata
-}